Orthogonal photoswitching of heterobivalent azobenzene glycoclusters: the effect of glycoligand orientation in bacterial adhesion

• Leon M. Friedrich and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2025, 21, 736–748, doi:10.3762/bjoc.21.57

• the structural determinants of the recognition process is a prerequisite for understanding and manipulating carbohydrate–protein interactions, such as in the inhibition of carbohydrate-specific bacterial adhesion. For receptor binding, glycoligands have to be properly oriented in three-dimensional

• every case, a terminal α-ᴅ-mannopyranoside unit is complexed within the FimH CRD. However, controlling the exact relative orientation of glycoligands in three-dimensional space is difficult in case of 1 and 2 as the degrees of freedom connected to the conformational dynamics are too large. Nevertheless

• the different isomeric states. The depicted RIP(MeMan) values are relative to the reference inhibitor MeMan tested on the same plate. Error bars of the inhibition of E. coli (GFP-PKL1162) adhesion to mannan reflect standard deviations (cf. Supporting Information File 1, Table S6). Three-dimensional

Synthesis of HBC fluorophores with an electrophilic handle for covalent attachment to Pepper RNA

• Raphael Bereiter and
• Ronald Micura

Beilstein J. Org. Chem. 2025, 21, 727–735, doi:10.3762/bjoc.21.56

• . HPLC traces were recorded with UV absorption by 260 nm. Structure-guided approach for engineering the (non-covalent) fluorescent light-up aptamer Pepper into its covalent counterpart [11]. a) Secondary structure of the Pepper aptamer [12]; b) chemical structure of the fluorophore HBC530 [7]; c) three

• -dimensional structure of the Pepper binding site with a bound HBC derivative (pdb code 7EOM). The hydrogen bond between N7 of guanine in position 41 (G41) and the hydroxy group of HBC is highlighted as gray dashed line [12]; d) concept for covalent attachment of HBC fluorophores to the N7 atom of G41 of the

Origami with small molecules: exploiting the C–F bond as a conformational tool

• Patrick Ryan,
• Ramsha Iftikhar and
• Luke Hunter

Beilstein J. Org. Chem. 2025, 21, 680–716, doi:10.3762/bjoc.21.54

• practitioner takes a piece of paper and imposes a series of folds in order to transform it into an object that has an intricate three-dimensional shape. This concept can also be applied in the molecular world. Starting with a flexible small molecule, a practitioner can impose certain changes to its chemical

• composition such that the new molecule has a better-defined three-dimensional shape. Such “small molecule origami” can offer practical benefits. For example, if a drug molecule is pre-organised into the target-binding conformation, it should exhibit the desirable twin characteristics of high potency (since

Photocatalyzed elaboration of antibody-based bioconjugates

• Marine Le Stum,
• Eugénie Romero and
• Gary A. Molander

Beilstein J. Org. Chem. 2025, 21, 616–629, doi:10.3762/bjoc.21.49

• remains largely unexplored. This is primarily because of the structural complexity of antibodies, which exhibit a three-dimensional architecture and numerous potential modification sites, making selective control of functionalization sites challenging. Nonetheless, photocatalytic approaches offer a unique

Synthesis, structure, ionochromic and cytotoxic properties of new 2-(indolin-2-yl)-1,3-tropolones

• Yurii A. Sayapin,
• Eugeny A. Gusakov,
• Inna O. Tupaeva,
• Alexander D. Dubonosov,
• Igor V. Dorogan,
• Valery V. Tkachev,
• Anna S. Goncharova,
• Gennady V. Shilov,
• Natalia S. Kuznetsova,
• Svetlana Y. Filippova,
• Tatyana A. Krasnikova,
• Yanis A. Boumber,
• Alexey Y. Maksimov,
• Sergey M. Aldoshin and
• Vladimir I. Minkin

Beilstein J. Org. Chem. 2025, 21, 358–368, doi:10.3762/bjoc.21.26

• cell parameters and reflection intensities for compound 7b (a three-dimensional set) were measured on an Xcalibur EOS autodiffractometer (Mo Kα irradiation, graphite monochromator, 150 K). Orange monoclinic crystals, chemical formula C21H14NO2Cl3, М = 418.68, a = 11.4480(3), b = 7.4883(2), с = 21.7720

Hydrogen-bonded macrocycle-mediated dimerization for orthogonal supramolecular polymerization

• Wentao Yu,
• Zhiyao Yang,
• Chengkan Yu,
• Xiaowei Li and
• Lihua Yuan

Beilstein J. Org. Chem. 2025, 21, 179–188, doi:10.3762/bjoc.21.10

• covalently linked polymers. So far, the design of such monomers has relied heavily on three-dimensional macrocycles, and the use of two-dimensional shape-persistent macrocycles for this purpose remains rather rare. Here, we demonstrate a dimerization motif based on a hydrogen-bonded macrocycle that can be

• photoluminescent materials [16]. In this regard, macrocycles emerged a decade ago as a “sticking” end for homo- and heterodifunctional monomers, enabling supramolecular polymerization [17]. So far, macrocycles that are applied to orthogonal self-assembly have been limited to three-dimensional rings, such as

Synthesis, structure and π-expansion of tris(4,5-dehydro-2,3:6,7-dibenzotropone)

• Yongming Xiong,
• Xue Lin Ma,
• Shilong Su and
• Qian Miao

Beilstein J. Org. Chem. 2025, 21, 1–7, doi:10.3762/bjoc.21.1

• definitively synthesized. The three-dimensional graphene-like carbons formed in a zeolite-template are the carbon forms that are the closest to carbon schwarzites so far [6][7]. Fragments of carbon schwarzites that retain their key structural characteristics are negatively curved polycyclic arenes [8][9

• ]. These are three-dimensional molecular nanocarbons that include heptagons [10][11][12][13][14], octagons [15][16][17][18], or even larger carbocycles. In theory, these fragments can serve as building blocks in a bottom-up approach to constructing carbon schwarzites [19][20]. To validate this concept, we

• approach to carbon schwarzites requires synthesizing of new negatively curved polycyclic arenes and expanding them to lager three-dimensional molecular nanocarbons. Compound 1 was recently used as a starting material for the synthesis of nonplanar polycyclic arenes, in particular, molecular models of cubic

Synthesis and antimycotic activity of new derivatives of imidazo[1,2-a]pyrimidines

• Dmitriy Yu. Vandyshev,
• Daria A. Mangusheva,
• Khidmet S. Shikhaliev,
• Kirill A. Scherbakov,
• Oleg N. Burov,
• Alexander D. Zagrebaev,
• Tatiana N. Khmelevskaya,
• Alexey S. Trenin and
• Fedor I. Zubkov

Beilstein J. Org. Chem. 2024, 20, 2806–2817, doi:10.3762/bjoc.20.236

• Tanimoto coefficient calculated from the MACCS descriptors for the selected compounds is <0.5, indicating that the chemical structure of compounds 4a–e and 5e is significantly different from voriconazole. The three-dimensional position of the selected compounds in the active site of the enzyme is shown in

Applications of microscopy and small angle scattering techniques for the characterisation of supramolecular gels

• Connor R. M. MacDonald and
• Emily R. Draper

Beilstein J. Org. Chem. 2024, 20, 2608–2634, doi:10.3762/bjoc.20.220

• could CLSM observe the initial kinetic self-sorting of gelators, but it also showed that the homogenous mixture of NFs and CFs can undergo a higher level of self-sorting, resulting in macroscopic phase separation (Figure 4). To gather a three-dimensional surface profile of a material, AFM utilises a

• which is not necessarily the same as the bulk morphology. Cryo-TEM can better probe three-dimensional structures, however, it is important to consider the additional artifacts that arise in cryo-TEM sample preparation. Cryo-TEM requires a thin film sample which can be difficult to prepare with a gel

Computational toolbox for the analysis of protein–glycan interactions

• Ferran Nieto-Fabregat,
• Maria Pia Lenza,
• Angela Marseglia,
• Cristina Di Carluccio,
• Antonio Molinaro,
• Alba Silipo and
• Roberta Marchetti

Beilstein J. Org. Chem. 2024, 20, 2084–2107, doi:10.3762/bjoc.20.180

• , especially in bacterial glycans, makes the structural and conformational analysis of glycans extremely difficult, posing a considerable challenge when employing conventional structural biology methods for glycan analysis [10][12]. Nevertheless, understanding the three-dimensional structure of glycans is

• -known family of GBPs is constituted by the lectins, ubiquitous receptors that exhibit the ability to specifically recognise different carbohydrates through their well-defined binding pocket and they conserved three-dimensional structure similarities [32]. On the other hand, GAG-binding proteins, which

• state can be performed with the same tools described below in the protein–ligand interactions section. Computational tools to study proteins in the free state Knowledge on the three-dimensional structure of a protein is essential for understanding the functions and the dynamics of protein interactions

Methyltransferases from RiPP pathways: shaping the landscape of natural product chemistry

• Maria-Paula Schröder,
• Isabel P.-M. Pfeiffer and
• Silja Mordhorst

Beilstein J. Org. Chem. 2024, 20, 1652–1670, doi:10.3762/bjoc.20.147

• cyclised core peptide to exert its effects on the precursor peptide. Furthermore, SAM was shown to be an obligate co-substrate for OlvSA [71]. Crystallographic data of OlvSA is not yet available. The predicted three-dimensional structure displays substantial differences from the crystal structure of LahSB

• stereochemistry has not been fully determined yet, one of two proposed positional isomers of the biaryl link between Trp2 and Trp3 is depicted [66]. The three-dimensional structures of the conventional O-MTs OlvSA (model structure calculated by Colabfold [75] and visualised by PyMOL [76]) and LahSB with bound SAH

• core peptide is coloured in orange. Methylation of the backbone is highlighted in green. B) Three-dimensional structure of the OphMA homodimer, PDB ID: 6TCS (https://doi.org/10.2210/pdb6tsc/pdb) [99]. Overview of the protein architectures and core peptide compositions of borosin N-MTs as defined by

Polymer degrading marine Microbulbifer bacteria: an un(der)utilized source of chemical and biocatalytic novelty

• Weimao Zhong and
• Vinayak Agarwal

Beilstein J. Org. Chem. 2024, 20, 1635–1651, doi:10.3762/bjoc.20.146

• [48]. The three-dimensional structure of CEST revealed that it belongs to the α/β-class of proteins consisting of a central six-stranded β-sheet flanked by eight α-helices. Site-directed mutagenesis indicated that a Ser-His-Glu catalytic triad was essential for the enzyme activity [48]. Another cold

Spin and charge interactions between nanographene host and ferrocene

• Akira Suzuki,
• Yuya Miyake,
• Ryoga Shibata and
• Kazuyuki Takai

Beilstein J. Org. Chem. 2024, 20, 1011–1019, doi:10.3762/bjoc.20.89

• three-dimensional disordered network of nanographite domains, each of which is a loose stack of 3–4 nanographene sheets with a mean in-plane size of 2–3 nm. ACFs have huge specific surface areas (about 2000 m2/g [24][25]) due to the presence of nanopores of ca. 1 nm in diameter between the nanographite

(Bio)isosteres of ortho- and meta-substituted benzenes

• H. Erik Diepers and
• Johannes C. L. Walker

Beilstein J. Org. Chem. 2024, 20, 859–890, doi:10.3762/bjoc.20.78

• different related tri- and polysubstituted scaffolds have been synthesised in the last few years, with the aim of providing more saturated and three-dimensional molecules for drug discovery. While many of them have not been explicitly suggested as potential isosteres for variously substituted benzenes, they

Synthesis of new representatives of A₃B-type carboranylporphyrins based on meso-tetra(pentafluorophenyl)porphyrin transformations

• Victoria M. Alpatova,
• Evgeny G. Rys,
• Elena G. Kononova and
• Valentina A. Ol'shevskaya

Beilstein J. Org. Chem. 2024, 20, 767–776, doi:10.3762/bjoc.20.70

• meso-pentafluorophenyl-substituted porphyrins. Carboranes, due to their unique physical and chemical properties such as high chemical and biological stability [28][29], three-dimensional aromaticity [30][31], low toxicity [28], high hydrophobicity, and enriched boron content [32][33] are perspective

Entry to new spiroheterocycles via tandem Rh(II)-catalyzed O–H insertion/base-promoted cyclization involving diazoarylidene succinimides

• Alexander Yanovich,
• Anastasia Vepreva,
• Ksenia Malkova,
• Grigory Kantin and
• Dmitry Dar’in

Beilstein J. Org. Chem. 2024, 20, 561–569, doi:10.3762/bjoc.20.48

• modern drug design [1][2]. They are known to promote higher success rates, when targeting three-dimensional protein molecules [3][4]. Furthermore, a wide variety of spirocyclic fragments can be spotted in natural products [5]. The aspects mentioned unveil the development of synthetic methodologies

Green and sustainable approaches for the Friedel–Crafts reaction between aldehydes and indoles

• Periklis X. Kolagkis,
• Eirini M. Galathri and
• Christoforos G. Kokotos

Beilstein J. Org. Chem. 2024, 20, 379–426, doi:10.3762/bjoc.20.36

Elucidating the glycan-binding specificity and structure of Cucumis melo agglutinin, a new R-type lectin

• Jon Lundstrøm,
• Emilie Gillon,
• Valérie Chazalet,
• Nicole Kerekes,
• Antonio Di Maio,
• Ten Feizi,
• Yan Liu,
• Annabelle Varrot and
• Daniel Bojar

Beilstein J. Org. Chem. 2024, 20, 306–320, doi:10.3762/bjoc.20.31

• no binding to unsubstituted galactose, we rather hypothesized the existence of specific interactions made with the C2-substituents, that did not exist in other R-type lectins such as RCA1. To determine this, we set out to resolve the detailed three-dimensional structure of CMA1 via X-ray

Tying a knot between crown ethers and porphyrins

• Maksym Matviyishyn and
• Bartosz Szyszko

Beilstein J. Org. Chem. 2023, 19, 1630–1650, doi:10.3762/bjoc.19.120

• synthesis of three-dimensional cryptands by Lehn [5], and spherands by Cram [6]. Later on, various classes of macrocyclic compounds were designed, demonstrating remarkable features in areas spreading from simple coordination chemistry [7], through host–guest chemistry, sensing [8], biomedicine [9], and

• molecules, e.g., catenanes and rotaxanes (Figure 16C). The formation of such compounds would eventually result in the formation of a unique group of three-dimensional ligands with co-existing porphyrin-like and crown ether cavities. The perspective article has highlighted the wide range of crown ether

Cyclodextrins permeabilize DPPC liposome membranes: a focus on cholesterol content, cyclodextrin type, and concentration

• Ghenwa Nasr,
• Hélène Greige-Gerges,
• Sophie Fourmentin,
• Abdelhamid Elaissari and
• Nathalie Khreich

Beilstein J. Org. Chem. 2023, 19, 1570–1579, doi:10.3762/bjoc.19.115

• of the native CDs, their three-dimensional structure, and their dimensions (n = 6, 7, and 8 glucopyranose units for α-, β-, and γ-CD, respectively). This figure was reused by permission from Springer Nature from [21]. (“130 years of cyclodextrin discovery for health, food, agriculture, and the

Aromatic C–H bond functionalization through organocatalyzed asymmetric intermolecular aza-Friedel–Crafts reaction: a recent update

• Anup Biswas

Beilstein J. Org. Chem. 2023, 19, 956–981, doi:10.3762/bjoc.19.72

• the reaction partners in a highly ordered three dimensional transition state through noncovalent interactions (like H-bonding, π–π interactions) thus promoting the stereoselective reaction. Examples of covalent bonding organocatalysts are amines [6][7], N-heterocyclic carbenes [8][9], phosphines [10

• carbonyl oxygen of 69 in the ternary complex, thus bringing more rigidity in the three dimensional transition state (Scheme 18) [46]. In 2021, Chen and co-workers documented a chiral phosphoric acid P17-catalyzed aza-Friedel–Crafts process between racemic 2,3-dihydroisoxazol-3-ol derivatives 76 and

Construction of hexabenzocoronene-based chiral nanographenes

• Ranran Li,
• Di Wang,
• Shengtao Li and
• Peng An

Beilstein J. Org. Chem. 2023, 19, 736–751, doi:10.3762/bjoc.19.54

• glum of (P,P,M/M,M,P)-117 was measured as 2 × 10−4. Cyclooctatetraphenylene (COT-Ph) is a π-conjugated scaffold, whose three-dimensional (3D) geometry is based on its saddle shape. Martín and co-workers reported the 3D NG 121 by the introduction of four HBC units into COT-Ph [60]. As shown in Scheme 14

• = 1375 M−1 cm−1 at 573 nm at 430 nm) for enantiopure 125 was obtained. In 2019, Wang and co-workers reported the largest atomically precise three-dimensional conjugated chiral nanographene propeller 128, representing the largest three-dimensional conjugated polyaromatics everprepared using scalable

• exploit three-dimensional aesthetic structures. The continuously developed novel structures contented our interests and curiosity. To further tune the optoelectronic or photophysical properties of nanographenes for real applications, heteroatom doping was found to be an effective strategy. The

A novel spirocyclic scaffold accessed via tandem Claisen rearrangement/intramolecular oxa-Michael addition

• Anastasia Vepreva,
• Alexander Yanovich,
• Dmitry Dar’in,
• Grigory Kantin,
• Alexander Bunev and
• Mikhail Krasavin

Beilstein J. Org. Chem. 2022, 18, 1649–1655, doi:10.3762/bjoc.18.177

• higher success rates [2] in discovering new cases of affinity towards a three-dimensional protein molecule [3]. Spirocycles of all sorts are omnipresent in the natural product realm [4]. Among the approved medicines the following spirocyclic molecules are notable: spironolactone for heart disease and

Characterization of a new fusicoccane-type diterpene synthase and an associated P450 enzyme

• Jia-Hua Huang,
• Jian-Ming Lv,
• Liang-Yan Xiao,
• Qian Xu,
• Fu-Long Lin,
• Gao-Qian Wang,
• Guo-Dong Chen,
• Sheng-Ying Qin,
• Dan Hu and
• Hao Gao

Beilstein J. Org. Chem. 2022, 18, 1396–1402, doi:10.3762/bjoc.18.144

• might adopt a similar strategy as MgMS to initiate C2,6 cyclization though protonation at C2 by bulky water. To obtain further insights into the C2,6-cyclization process of TadA, its three-dimensional (3D) protein structure was constructed with SWISS-MODEL using PaFS (PDB entry 5er8) as the template

Cytochrome P450 monooxygenase-mediated tailoring of triterpenoids and steroids in plants

• Karan Malhotra and
• Jakob Franke

Beilstein J. Org. Chem. 2022, 18, 1289–1310, doi:10.3762/bjoc.18.135

• sterol scaffolds have drastically different three-dimensional shapes. For this reason, CYPs are typically specific to a certain group of triterpenoid scaffolds. Hence, we summarised our list of 149 triterpenoid/steroid CYPs (Table 1) according to their target scaffold. Figure 3 covers plant CYPs acting